Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_012589851.1 MSIL_RS04185 3-hydroxybutyrate dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_000021745.1:WP_012589851.1 Length = 261 Score = 118 bits (296), Expect = 1e-31 Identities = 85/255 (33%), Positives = 126/255 (49%), Gaps = 8/255 (3%) Query: 19 LKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDI-QAQKVEAVAAHWR-ERGADVHALQ 76 LK + ++TG+ GIG AI FA A + I+ + A +EA A + G Sbjct: 3 LKSRNAIVTGSTSGIGLAIAREFAKDGANVTINGLGDAAAIEAERAKIEADFGVKAAYSP 62 Query: 77 ADVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 A+++K ++++AM A + G +D+LVN AG+ + + W AI+L A++ Sbjct: 63 ANMTKPEEIRAMVTDAEKAFGSVDILVNNAGIQHVAPIEDFPIDTWNLIIAINLSAAFHA 122 Query: 137 CKAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 A +P M + G II+ AS HS P Y AKHG+ GLT+ +E A GV VN Sbjct: 123 IAAAIPGMKARKWGRIISTASAHSKVASPFKSAYVSAKHGIDGLTKTAALELATFGVTVN 182 Query: 197 AIAPGYIETQL-NVDYWNGFADPHAERQRA-----LDLHPPRRVGQPIEVAMTAVFLASD 250 I+PGY+ T L + A H R++ L P ++ +VA A FL +D Sbjct: 183 CISPGYVWTPLVEKQIPDTMASRHLTREQVINDVLLTAQPTKQFVTVDQVAALAAFLCTD 242 Query: 251 EAPFINASCITIDGG 265 A I S I+IDGG Sbjct: 243 AASQITGSNISIDGG 257 Lambda K H 0.321 0.137 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 147 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 261 Length adjustment: 25 Effective length of query: 247 Effective length of database: 236 Effective search space: 58292 Effective search space used: 58292 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory